title: Day 10 (H1 hEB cells)

city: Baltimore

first: Wayne

last: Yu

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

description: Individual sample

hyb_protocol: Using Agilent hybridization chambers and oven following manufacturer's protocol (65oC for 17 hours)

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Processed signal intensities are imported into GeneSpring Gx 7.3 and normalized to the median signal intensities of each arrays. Intensities of replicate probes are represented as single value of average.

source_name: Human stem cells differentiated under conditions

label_protocol: 400 ng total Rna is amplified and labeled using Agilent low in put RNA amplification and labeling kit and Cy3-CTP (Perkin Elmer) following manufacturer's protocol.

growth_protocol: The hESC line H1 (NIH code: WA01) was maintained on irradiated primary murine embryonic feeders (PMEF), and hEB were formed from hESC clumps in semisolid, serum-supplemented medium, exactly as previously described (Zambidis et al., 2005). Twenty-four hours after hESC plating, (Day 2) simple hEB were harvested, washed, re-suspended in PBS in 50-ml conical tubes, and collected by gentle gravity settling for 2-3 minutes. Formed hEB were re-suspended into 6-well ultra-non-adherent plates (Corning) at ~100-200 hEB/ml in SF liquid differentiation medium (SF LDM), consisting of serum-free expansion medium (SFEM, StemCell Technologies) supplemented with 50 ug/ml ascorbic acid (SIGMA), 1% EXCYTE, 0.5% insulin/transferrin/selenium (Invitrogen), 3% PFHM-II (Invitrogen), and penicillin/streptomycin (SIGMA). Various combinations of human growth factors (all from R&D Systems, Peprotech, or Invitrogen) were added directly into SF LDM at 2-20 days of hEB development: BMP4 (50 ng/ml), VEGF (50 ng/ml), FGF1 (50 ng/ml+ 5ug/ml heparin sulfate, SIGMA), FGF2 (50 ng/ml+ 5 ug/ml heparin sulfate), murine Nodal (50 ng/ml), IGF-II (50 ng/ml), murine wnt3a (50 ng/ml), and activin A (50 ng/ml). hEB cultures were fed by hemi-depletion and replacement of medium every 2-3 days with fresh SF LDM and GFs. To expand hEB-derived hematopoietic progenitors, enzymatically-digested (Accutase, SIGMA) day 9-10 hEB clumps, differentiated as above, were transferred into SF LDM and allowed to adhere to gelatinized tissue culture plates. SF cultures were supplemented with various hematopoietic inductive factors including: BMP4 (50 ng/ml), SCF (50 ng/ml), Flt3L (50 ng/ml), TPO (50 ng/ml), GM-CSF (50 ng/ml), G-CSF (50 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml), VEGF (20 ng/ml), EPO (2 units/ml), FGF1 (10 ng/ml) and FGF2 (10 ng/ml).

extract_protocol: Total RNA are isolated from cell pellets using TriZol reagent(Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up.


title: Endothelial cells from left iliac artery, rep 4

status: Public on Aug 23 2008

type: RNA

city: Durham

first: Ji

last: Zhang

state: NC

address: Room 136 Hudson Hall

department: Department of Biomedical Engineering

country: USA

institute: Duke University

description: Endothelial cells were freshly harvest from right coronary, left and right iliac arteries from four pigs.

hyb_protocol: • Make hybridization buffer fresh each time.  • Add 38 ul hybridization buffer to 12 ul fragmented Cy Dye labeled aa-aRNA.  • Add 1ul each poly dA and appropriate Cot-1 DNA.  • Heat at 95ºC for 2 minutes and put on ice to cool down.  • Mix well and load sample to the array slide with lifter cover slip.  • Hybridize overnight in 42ºC water bath.

scan_protocol: Scanned by GenePix 4000B and quantified using GenePix software

data_processing: LOWESS normalized, inlcude genes with signal in at least 8 of the 12 arrays, Agilent GeneSpring GX was used.

molecule: total RNA

organism: Sus scrofa

source_name: left iliac endothelial cells

label_protocol: Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion). two rounds of amplification were performed, and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes, and reference RNA sample was labeled with Cy3 dyes.

growth_protocol: Reference endothelial cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum. Passage 3 cells were used.

extract_protocol: Qiagen RNeasy Micro kit following manufacturer's protocol

tag: Animal 4

source_name: reference RNA

tag: cultured porcine aortic endothelial cells (passage 3)


title: Day 3 (H1 hEB cells)

state: MD

description: Individual sample

organism: Homo sapiens

tag: Human stem cells differentiated under conditions


title: Day 7 (H1 hEB cells)

description: Individual sample


title: Endothelial cells from right coronary artery, rep 4

source_name: right coronary endothelial cells


title: Liver_PB_CAR/PXR_rep5

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: No additional data.

hyb_protocol: Sterolgene V1 slides were washed before hybridization at room temperature 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. Samples were denatured and hybridized in 3xSSC and 0.2% SDS hybridization buffer at 65˚C for 16 hours using humidified hybridization chambers (HybChambers, GeneMachines). After hybridizations slides were washed at room temperature for 5 min in 2xSSC and 0.5% SDS, followed by 5 min in 0.5xSSC, then 5 min in 0.05xSSC and dried by centrifugation.

scan_protocol: Slides were scanned with Affimetrix 428 Array Scanner using Software Jaguar 2.0. Images were analyzed Gene Pix Pro 6.0 (Molecular Devices Corporation). The median feature and local background intensities were extracted together with the estimates of their standard deviation.

data_processing: Features were filtered out according to the following criteria: coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) above 0.5 and foreground to background ratio above 1.5. Saturated features were removed. Log2 ratios were normalized using LOESS fit to spike in control RNAs and housekeeping controls. Filtration and normalization was done in Orange software. Normalized log ratios can be compared across samples.

organism: Mus musculus

source_name: Liver, phenobarbital-treated

label_protocol: Lucidea Universal scorecard (GE Helthcare) was added as an universal reference for microarray experiment. 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol.

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were maintained in 12-hour light/12-hour dark cycle.

treatment_protocol: Animals were injected i.p. with phenobarbital (100mg/kg). After 12h they were sacrificed.

tag: Genetic background

value: CAR/PXR deficient

tag: Strain

tag: Gender

value: male

tag: Age

value: 9-12 weeks

tag: Tissue

value: liver

tag: Treatment

value: 100 mg/kg phenobarbital

source_name: Liver, untreated CAR/PXR pool

label_protocol: Firefly luciferase (Promega) was added as an universal reference for microarray experiment. 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). Spectrofotometer (Nanodrop) was used to monitor the quality of RNA. RNAs from 6 replicates were pooled and used for hybridization.

treatment_protocol: Animals were injected i.p. vehicle (5% DMSO in corn oil). After 12h they were sacrificed.

value: 5% DMSO in corn oil


title: Liver_PB_CAR_rep4

description: No additional data.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). Spectrofotometer (Nanodrop) was used to monitor the quality of RNA.

value: CAR deficient

source_name: Liver, untreated CAR pool


title: Liver_PB_PXR_rep1

description: No additional data.

source_name: Liver, phenobarbital treated

value: PXR deficient

source_name: Liver, untreated PXR pool


title: Liver_PB_CAR/PXR_rep2

description: No additional data.

source_name: Liver, untreated, CAR/PXR pool


title: Liver_PB_CAR/PXR_rep4

description: No additional data.


title: Endothelial cells from right iliac artery, rep 4

source_name: right iliac endothelial cells


title: Endothelial cells from right iliac artery, rep 3

tag: Animal 3


title: Day 0 (undifferentiated H1 hESC)

description: Individual sample

source_name: Human undifferentiated embryonic stem cells


title: Liver_PB_CAR_rep1

description: No additional data.


title: Liver_PB_CAR/PXR_rep3

description: No additional data.


title: Endothelial cells from left iliac artery, rep 3


title: Liver_PB_CAR/PXR_rep1

description: No additional data.


title: Liver_PB_CAR/PXR_rep6

description: No additional data.


title: Liver_PB_WT_rep6

description: No additional data.

value: wild type (WT)

tag: Age:9-12 weeks

source_name: Liver, untreated WT pool


title: Liver_PB_WT_rep5

description: No additional data.


title: Liver_PB_WT_rep4

description: No additional data.


title: Endothelial cells from right coronary artery, rep 3


title: Endothelial cells from right iliac artery, rep 2

tag: Animal 2


title: Endothelial cells from right iliac artery, rep 1

tag: Animal 1


title: Liver_PB_WT_rep2

description: No additional data.


title: Endothelial cells from left iliac artery, rep 1


title: Day 5 (H1 hEB cells)

description: Individual sample


title: Liver_PB_WT_rep3

description: No additional data.


title: Endothelial cells from right coronary artery, rep 1


title: Liver_PB_WT_rep1

description: No additional data.


title: Endothelial cells from left iliac artery, rep 2


title: CN_AML Patient 162 (U133B)

status: Public on Aug 22 2008

city: Munich

first: Klaus

middle: H

last: Metzeler

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University of Munich

description: AML, normal karyotype (training set) FAB M2; age =79 years; OS = 175 days; status (0=alive/1=dead): 1

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the variance stabilizing normalization algorithm, and probe set expression values were calculated by the median polish method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set  summarization.

label: biotin

source_name: bone marrow mononuclear cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from bone marrow (BM) or peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow or peripheral blood mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML) with a normal karyotype


title: CTRL_coIP_ESP_2

type: mixed

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

description: Intensity ratios of labelled coIP-RNA (channel 2) divided by DNA (channel 1) signals minus respective background signals. Total array is 25 blocks arranged in 5X5 configuration.

hyb_protocol: Labelled samples were resuspended in hybridization buffer (1 M NaCl; 50 mM Mes, pH 7.0; 20% formamide; 1% Triton X-100). The hybridization was performed in microarray chambers (Agilent Technologies) and rotated at 55° over 48 h. The arrays were then washed with Wash 1 [6× standard saline phosphate/EDTA (0.18 M NaCl/10 mM phosphate, pH 7.4/1 mM EDTA] (SSPE)/0.005% N-lauryl sarcosine] and Wash 2 (0.06% SSPE/0.18% polyethylene glycol 200), both for 5 min at room temperature.

scan_protocol: Axon GenePix Autoloader 4200AL 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Image analysis was performed using the BlueFuse software (BlueGnome). Block-median data centring was then performed in BlueFuse to obtain a median ratio (Cy5/Cy3) for each of the 25 blocks equal to 1. This step generated the AMPCH1 and AMPCH2 values. When comparing AMPCH1 and AMPCH2 values from different hybridisations, we observed slight deviations which were dependent on gene expression levels. These were corrected using the Loess function in R (Limma package), thus generating values found in the VALUE column.

molecule: genomic DNA

organism: Salmonella enterica

source_name: Reference genomic DNA

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: S. Typhimurium grown to stationary phase in LB-broth

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)

tag: Salmonella enterica serovar Typhimurium SL1344

molecule: other

source_name: Control Hfq-RNA coimmunoprecipitate

label_protocol: 100-200 ng immunoprecipitated RNA was reverse transcribed into ssDNA by random priming using 200 U of AffinityScript (Stratagene) at 50°C. RNA was subsequently hydrolysed by adding 0.1N NaOH and incubating the sample for 10min at 70°. The alkali was neutralised adding 0.1N HCl. As all the nucleotide probes present on the microarrays used (Platform GPL5791) correspond to the ‘+’-strand, prior to the incorporation of the fluorescent label we converted ssDNA to dsDNA using random priming and the klenow fragment from the BioPrime DNA labelling system (Invitrogen). Cy-dye incorporation into cDNA was performed using the 'Direct labelling of DNA' protocol that can be found at http://www.ifr.bbsrc.ac.uk/safety/microarrays/protocols.html. All clean up steps were performed by ethanol precipitation rather than by using spin columns to avoid loosing the shorter RNA/cDNA species.

extract_protocol: Strains were grown in L-broth under normal aeration at 37°C up to ESP (OD600 = 2.0). Coimmunoprecipitated RNA was isolated following the protocol described in: Pfeiffer et al. (2007); Molecular microbiology 66, 1174-1191.


title: CN_AML Patient 161 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =53 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CTRL_coIP_ESP_1


title: HFQ::FLAG_coIP_ESP_1

source_name: Hfq3xFLAG-RNA coimmunoprecipitate

tag: Salmonella enterica serovar Typhimurium SL1344 hfq3xFLAG


title: CN_AML Patient 157 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =61 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 159 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =53 years; OS = 51 days; status (0=alive/1=dead): 1


title: CN_AML Patient 160 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =56 years; OS = 676 days; status (0=alive/1=dead): 0


title: HFQ::FLAG_coIP_ESP_2


title: CN_AML Patient 158 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =61 years; OS = 223 days; status (0=alive/1=dead): 1


title: CN_AML Patient 161 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =53 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 154 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =57 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 158 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =61 years; OS = 223 days; status (0=alive/1=dead)


title: CN_AML Patient 151 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =40 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 155 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =59 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 153 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =43 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 163 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =32 years; OS = 916 days; status (0=alive/1=dead): 0


title: Endothelial cells from right coronary artery, rep 2


title: CN_AML Patient 149 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =65 years; OS = 233 days; status (0=alive/1=dead): 1


title: CN_AML Patient 156 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =29 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 159 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =53 years; OS = 51 days; status (0=alive/1=dead)


title: CN_AML Patient 160 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =56 years; OS = 676 days; status (0=alive/1=dead)


title: CN_AML Patient 148 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =67 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 152 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =38 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 153 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =43 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 156 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =29 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 146 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =68 years; OS = 559 days; status (0=alive/1=dead): 1


title: CN_AML Patient 142 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =75 years; OS = 41 days; status (0=alive/1=dead): 1


title: CN_AML Patient 141 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =55 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 145 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =68 years; OS = 1113 days; status (0=alive/1=dead): 0


title: CN_AML Patient 140 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =37 years; OS = 999 days; status (0=alive/1=dead): 1


title: CN_AML Patient 147 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =62 years; OS = 209 days; status (0=alive/1=dead): 0


title: CN_AML Patient 148 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =67 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 154 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =57 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 144 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =69 years; OS = 192 days; status (0=alive/1=dead): 1


title: CN_AML Patient 146 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =68 years; OS = 559 days; status (0=alive/1=dead)


title: CN_AML Patient 157 (U133A)

description: AML, normal karyotype (training set) FAB M4; age =61 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 139 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =54 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 138 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =66 years; OS = 304 days; status (0=alive/1=dead): 1


title: CN_AML Patient 151 (U133A)

description: AML, normal karyotype (training set) FAB M5; age =40 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 150 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =71 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 143 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =44 years; OS = 352 days; status (0=alive/1=dead): 1


title: CN_AML Patient 136 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =67 years; OS = 137 days; status (0=alive/1=dead): 1


title: CN_AML Patient 137 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =36 years; OS = 326 days; status (0=alive/1=dead): 1


title: CN_AML Patient 145 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =68 years; OS = 1113 days; status (0=alive/1=dead)


title: CN_AML Patient 144 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =69 years; OS = 192 days; status (0=alive/1=dead)


title: CN_AML Patient 150 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =71 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 143 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =44 years; OS = 352 days; status (0=alive/1=dead)


title: CN_AML Patient 142 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =75 years; OS = 41 days; status (0=alive/1=dead)


title: CN_AML Patient 135 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =24 years; OS = 79 days; status (0=alive/1=dead): 1


title: CN_AML Patient 132 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =20 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 134 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =66 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 140 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =37 years; OS = 999 days; status (0=alive/1=dead)


title: CN_AML Patient 133 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =70 years; OS = 19 days; status (0=alive/1=dead): 1


title: CN_AML Patient 138 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =66 years; OS = 304 days; status (0=alive/1=dead)


title: CN_AML Patient 131 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =65 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 128 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =65 years; OS = 148 days; status (0=alive/1=dead): 1


title: CN_AML Patient 139 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =54 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 127 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =59 years; OS = 31 days; status (0=alive/1=dead): 1


title: CN_AML Patient 129 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =17 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 130 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =74 years; OS = 284 days; status (0=alive/1=dead): 1


title: CN_AML Patient 137 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =36 years; OS = 326 days; status (0=alive/1=dead)


title: GFP RNA from 18 hpf (Flk)

city: Milwaukee

first: Ramani

last: Ramchandran

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: Cy3 labeled cRNA from GFP+ cells of 24 hpf Flk embryo was spotted on the array

hyb_protocol: The hybridization and stringency washes were performed on a Tecan HS4800 automated hybstation.Hybridization buffer was the Ocimum Biosolutions salt-based hyb buffer (1180-200000). Washes were done with 2xSSC, 0.1% SDS, 1xSSC, and 0.5x SSC, respectively.

scan_protocol: The dried arrays were scanned using an Affymetrix 428 array scanner at 10 micrometer resolution at three different pmt gain settings per slide, creating three tiff images per slide.

data_processing: Ocimum proprietary software MAVI was used to combine the datasets of the three different tiff images of each slide to one dataset. Linear regression algorithms are used to both extend the dynamic range, and avoid saturation (upper end) and signal deterioration due to scanner detection limits at the lower end). MAVI files contain both raw data as well as background corrected and/or normalized intensities. The most important data columns have the ending .Ic3 (=background corrected intensities, no normalization) and .Ic3pc (=normalized and background corrected intensities, suitable to compare across multiple slides).

organism: Danio rerio

source_name: Whole zebrafish larvae

label_protocol: The sample preparation (amplification and labeling) was performed using the AmpTec ExpressArt kit (Nano version). Two rounds of amplification were performed. Then the cRNA samples were labeled with Cy3 (Amersham) and fragmented (see aminoallyl supplement of the AmpTec kit).

growth_protocol: Zebrafish were grown and maintained at 28C until the desired stage.

extract_protocol: Tg(Fli1:EGFP) fish were dissociated at appropriate time points and GFP positive cells were FACS sorted and collected for RNA isolation.

treatment_protocol: No treatment of fish prior to dissociation of GFP cells from fish. The protocol for cell dissociation has been published previously (Kaur et al., JBC 2006).

tag: GFP only (Flk)


title: CN_AML Patient 141 (U133A)

description: AML, normal karyotype (training set) FAB M2; age =55 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 124 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =58 years; OS = 24 days; status (0=alive/1=dead): 1


title: CN_AML Patient 125 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =44 years; OS = 486 days; status (0=alive/1=dead): 0


title: CN_AML Patient 126 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =66 years; OS = 693 days; status (0=alive/1=dead): 1


title: CN_AML Patient 149 (U133A)

description: AML, normal karyotype (training set) FAB M1; age =65 years; OS = 233 days; status (0=alive/1=dead): 1


title: GFP RNA from 18 hpf (Fli)

description: Cy3 labeled cRNA from GFP+ cells of 18 hpf Fli embryo was spotted on the array

tag: GFP only (Fli)


title: CN_AML Patient 123 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =83 years; OS = 127 days; status (0=alive/1=dead): 1


title: GFP RNA from 24 hpf (Fli)

description: Cy3 labeled cRNA from GFP+ cells of 24 hpf Fli embryo was spotted on the array


title: GFP RNA from 28 hpf (Fli)

description: Cy3 labeled cRNA from GFP+ cells of 28 hpf Fli embryo was spotted on the array


title: Total RNA from 24 hpf

description: Total Cy3 labeled cRNA from 24 hpf embryo was spotted on the array

tag: Total RNA from 24 hpf


title: CN_AML Patient 121 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =49 years; OS = 840 days; status (0=alive/1=dead): 0


title: Total RNA from 18 hpf

description: Total Cy3 labeled cRNA from 18 hpf embryo was spotted on the array

tag: Total RNA from 18 hpf


title: CN_AML Patient 122 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =71 years; OS = 794 days; status (0=alive/1=dead): 0


title: Tomato-leaves

first: Frank

last: Schwach

address: University of East Anglia

department: School of Computing Sciences

institute: University of East Anglia

description: Total endogenous small RNAs from Solanum lycopersicum cv. MicroTom young leaves

data_processing: removed 5' and 3' adapters. Sequences without adapters were discarded.

organism: Solanum lycopersicum

growth_protocol: Plants were grown under 16h light in the greenhouse

extract_protocol: Total RNA was extracted from leaves and further purifed on polyacrylamide gels

tag: Mature leaves


title: CN_AML Patient 128 (U133A)

description: AML, normal karyotype (training set) FAB M2; age =65 years; OS = 148 days; status (0=alive/1=dead): 1


title: CN_AML Patient 119 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =67 years; OS = 114 days; status (0=alive/1=dead): 0


title: CN_AML Patient 124 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =58 years; OS = 24 days; status (0=alive/1=dead)


title: CN_AML Patient 120 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =32 years; OS = 849 days; status (0=alive/1=dead): 0


title: Mouse MF1-075

city: los angeles

first: anatole

last: ghazalpour

state: CA

address: 675 charles young dr south

institute: UCLA

description: Whole genome association analysis of gene expression traits in an outbred mouse population, the MF1 stock.

hyb_protocol: 800 ng of labeled cRNA product is hybridized to prepared whole genome arrays and allowed to incubate overnight ( 16 –20 hrs) at 55 degrees C.  Arrays are washed then stained with Cy3 labeled streptavadin. Excess stain is removed by washing and the arrays are dried and scanned on an Illumina BeadScan con-focal laser scanner.

data_processing: data were scaled and normalized using the rank invariant method in the Beadstudio software v. 1.5.1.3. (Illumina Inc.)

source_name: Liver, highfat diet 14 weeks

label_protocol: RNA samples queued for whole genome analysis using Illumina gene expression chips are first quanted using the ribogreen RNA quantitation kit. Samples are normalized to 11 ng per ul. 100 ng of normalized total RNA is used as a template for the synthesis of cDNA using Ambion cDNA synthesis kit AMIL1791. Newly synthesized  cDNA becomes the template for the amplification and biotinylation of cRNA . Labeled cRNA is quanted (ribogreen) and normalized to 77 ng per ul.

growth_protocol: mice were fed with chow diet till 19 weeks of age

extract_protocol: RNA extraction was performed on 25 mg of the liver tissue obtained from each animal at the time of sacrifice.  Total RNA was extracted using Qiagen’s RNeasy kit (cat# 74104).

treatment_protocol: mice were fed with high fat diet containing 42% fat and 0.15% cholesterol for ~14 weeks until they were sacrificed at 235 days of age.

tag: Strain

value: MF1 outbred stock, gender:female, age:235 days


title: Mouse MF1-081

scan_protocol: Illumina BeadScan con-focal laser scanner


title: Mouse MF1-122


title: CN_AML Patient 118 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =39 years; OS = 608 days; status (0=alive/1=dead): 0

source_name: peripheral blood mononuclear cells


title: Mouse MF1-123


title: CN_AML Patient 116 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =75 years; OS = 13 days; status (0=alive/1=dead): 1


title: Mouse MF1-077


title: Mouse MF1-080


title: Mouse MF1-076


title: CN_AML Patient 126 (U133A)

description: AML, normal karyotype (training set) FAB M2; age =66 years; OS = 693 days; status (0=alive/1=dead): 1


title: CN_AML Patient 115 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =57 years; OS = 575 days; status (0=alive/1=dead): 0


title: CN_AML Patient 125 (U133A)

description: AML, normal karyotype (training set) FAB M4; age =44 years; OS = 486 days; status (0=alive/1=dead): 0


title: Mouse MF1-078


title: Mouse MF1-079


title: CN_AML Patient 114 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =58 years; OS = 850 days; status (0=alive/1=dead): 0


title: Mouse MF1-120


title: Mouse MF1-074


title: CN_AML Patient 117 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =39 years; OS = 51 days; status (0=alive/1=dead): 0


title: CN_AML Patient 123 (U133A)

description: AML, normal karyotype (training set) FAB M2; age =83 years; OS = 127 days; status (0=alive/1=dead): 1


title: Mouse MF1-119


title: Tomato-fruits

description: Total endogenous small RNAs from Solanum lycopersicum cv. MicroTom fruits

source_name: Solanum lycopersicum cv. MicroTom fruits at various developmental stages

extract_protocol: Total RNA was extracted from fruits at various developmental stages and pooled. RNA extracts were purifed on polyacrylamide gels

tag: Pooled RNA extracts from fruits at developmental stages F1-3, F3-5, F5-7, F7-11, F11-14 (diameter in mm)


title: CN_AML Patient 122 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =71 years; OS = 794 days; status (0=alive/1=dead)


title: CN_AML Patient 121 (U133A)

description: AML, normal karyotype (training set) FAB M4; age =49 years; OS = 840 days; status (0=alive/1=dead): 0


title: Mouse MF1-118


title: Mouse MF1-117


title: Mouse MF1-129


title: CN_AML Patient 113 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =57 years; OS = 891 days; status (0=alive/1=dead): 0


title: CN_AML Patient 120 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =32 years; OS = 849 days; status (0=alive/1=dead)


title: Mouse MF1-131


title: Mouse MF1-115


title: CN_AML Patient 116 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =75 years; OS = 13 days; status (0=alive/1=dead)


title: CN_AML Patient 112 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =61 years; OS = 184 days; status (0=alive/1=dead): 1


title: CN_AML Patient 109 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =69 years; OS = 484 days; status (0=alive/1=dead): 1


title: CN_AML Patient 115 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =57 years; OS = 575 days; status (0=alive/1=dead)


title: CN_AML Patient 108 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =38 years; OS = 271 days; status (0=alive/1=dead): 1


title: Mouse MF1-127


title: Mouse MF1-128


title: Mouse MF1-103


title: CN_AML Patient 110 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =77 years; OS = 18 days; status (0=alive/1=dead): 1


title: Mouse MF1-105


title: Mouse MF1-116


title: Mouse MF1-124


title: Mouse MF1-125


title: CN_AML Patient 114 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =58 years; OS = 850 days; status (0=alive/1=dead)


title: CN_AML Patient 111 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =38 years; OS = 581 days; status (0=alive/1=dead): 0


title: CN_AML Patient 117 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =39 years; OS = 51 days; status (0=alive/1=dead)


title: Mouse MF1-102

description: Whole genome association analysis of gene expression traits in an outbred mouse population, the MF1 stock.


title: Mouse MF1-126


title: Mouse MF1-101


title: CN_AML Patient 119 (U133A)

description: AML, normal karyotype (training set) FAB M4; age =67 years; OS = 114 days; status (0=alive/1=dead): 0


title: CN_AML Patient 113 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =57 years; OS = 891 days; status (0=alive/1=dead)


title: CN_AML Patient 106 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =56 years; OS = 4 days; status (0=alive/1=dead): 1


title: CN_AML Patient 105 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =68 years; OS = 263 days; status (0=alive/1=dead): 1


title: Mouse MF1-098


title: Mouse MF1-055


title: Mouse MF1-100


title: Mouse MF1-099


title: CN_AML Patient 112 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =61 years; OS = 184 days; status (0=alive/1=dead)


title: CN_AML Patient 104 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =55 years; OS = 229 days; status (0=alive/1=dead): 1


title: CN_AML Patient 102 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =72 years; OS = 176 days; status (0=alive/1=dead): 1


title: Mouse MF1-052


title: Mouse MF1-053


title: CN_AML Patient 100 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =44 years; OS = 251 days; status (0=alive/1=dead): 1


title: CN_AML Patient 103 (U133B)

description: AML, normal karyotype (training set) FAB M0; age =44 years; OS = 741 days; status (0=alive/1=dead): 1


title: CN_AML Patient 110 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =77 years; OS = 18 days; status (0=alive/1=dead)


title: Mouse MF1-096


title: Mouse MF1-095


title: Mouse MF1-051


title: CN_AML Patient 109 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =69 years; OS = 484 days; status (0=alive/1=dead)


title: Mouse MF1-047


title: Mouse MF1-097


title: CN_AML Patient 107 (U133A)

description: AML, normal karyotype (training set) FAB M4; age =47 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 108 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =38 years; OS = 271 days; status (0=alive/1=dead)


title: CN_AML Patient 101 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =53 years; OS = 314 days; status (0=alive/1=dead): 1


title: Mouse MF1-049


title: Mouse MF1-050


title: Mouse MF1-093


title: CN_AML Patient 107 (U133B)

tag: AML, normal karyotype (training set) FAB M4; age =47 years; OS = 1176 days; status (0=alive/1=dead)


title: Mouse MF1-092


title: Mouse MF1-094


title: Mouse MF1-091


title: CN_AML Patient 105 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =68 years; OS = 263 days; status (0=alive/1=dead)


title: CN_AML Patient 98 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =40 years; OS = 33 days; status (0=alive/1=dead): 1


title: CN_AML Patient 97 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =75 years; OS = 91 days; status (0=alive/1=dead): 1


title: CN_AML Patient 99 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =53 years; OS = 872 days; status (0=alive/1=dead): 1


title: Mouse MF1-090


title: CN_AML Patient 104 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =55 years; OS = 229 days; status (0=alive/1=dead)


title: Mouse MF1-065


title: Mouse MF1-063


title: CN_AML Patient 96 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =78 years; OS = 62 days; status (0=alive/1=dead): 1


title: CN_AML Patient 102 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =72 years; OS = 176 days; status (0=alive/1=dead)


title: CN_AML Patient 95 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =60 years; OS = 452 days; status (0=alive/1=dead): 0


title: CN_AML Patient 101 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =53 years; OS = 314 days; status (0=alive/1=dead)


title: CN_AML Patient 94 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =20 years; OS = 340 days; status (0=alive/1=dead): 1


title: Mouse MF1-064

tag: Strain


title: Mouse MF1-059


title: Mouse MF1-110


title: Mouse MF1-056


title: CN_AML Patient 100 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =44 years; OS = 251 days; status (0=alive/1=dead)


title: Mouse MF1-112


title: Mouse MF1-109


title: CN_AML Patient 93 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =77 years; OS = 28 days; status (0=alive/1=dead): 1


title: Mouse MF1-057

description: Whole genome association analysis of gene expression traits in an outbred mouse population, the MF1 stock.


title: CN_AML Patient 99 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =53 years; OS = 872 days; status (0=alive/1=dead)


title: CN_AML Patient 97 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =75 years; OS = 91 days; status (0=alive/1=dead)


title: Mouse MF1-058


title: Mouse MF1-062


title: CN_AML Patient 92 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =71 years; OS = 289 days; status (0=alive/1=dead): 0


title: Mouse MF1-114


title: Mouse MF1-089


title: Mouse MF1-088


title: Mouse MF1-108


title: CN_AML Patient 90 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =40 years; OS = 250 days; status (0=alive/1=dead): 1


title: CN_AML Patient 89 (U133B)

description: AML, normal karyotype (training set) FAB M6; age =53 years; OS = 175 days; status (0=alive/1=dead): 1


title: CN_AML Patient 98 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =40 years; OS = 33 days; status (0=alive/1=dead)


title: Mouse MF1-106


title: CN_AML Patient 96 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =78 years; OS = 62 days; status (0=alive/1=dead)


title: CN_AML Patient 91 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =47 years; OS = 416 days; status (0=alive/1=dead): 1


title: Mouse MF1-087


title: Mouse MF1-085


title: Mouse MF1-086


title: Mouse MF1-084


title: CN_AML Patient 94 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =20 years; OS = 340 days; status (0=alive/1=dead)


title: CN_AML Patient 95 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =60 years; OS = 452 days; status (0=alive/1=dead)


title: CN_AML Patient 87 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =45 years; OS = 238 days; status (0=alive/1=dead): 1


title: CN_AML Patient 93 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =77 years; OS = 28 days; status (0=alive/1=dead)


title: CN_AML Patient 88 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =49 years; OS = 107 days; status (0=alive/1=dead): 1


title: Mouse MF1-082


title: Mouse MF1-083


title: CN_AML Patient 86 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =72 years; OS = 1176 days; status (0=alive/1=dead): 0


title: Mouse MF1-072


title: Mouse MF1-071


title: Mouse MF1-066


title: Mouse MF1-069


title: CN_AML Patient 92 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =71 years; OS = 289 days; status (0=alive/1=dead)


title: CN_AML Patient 83 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =67 years; OS = 157 days; status (0=alive/1=dead): 1


title: CN_AML Patient 84 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =39 years; OS = 1176 days; status (0=alive/1=dead): 0


title: Mouse MF1-068


title: Mouse MF1-073


title: CN_AML Patient 85 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =60 years; OS = 599 days; status (0=alive/1=dead): 1


title: CN_AML Patient 89 (U133A)

tag: AML, normal karyotype (training set) FAB M6; age =53 years; OS = 175 days; status (0=alive/1=dead)


title: Mouse MF1-070


title: Mouse MF1-043


title: CN_AML Patient 90 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =40 years; OS = 250 days; status (0=alive/1=dead)


title: Mouse MF1-045


title: CN_AML Patient 82 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =58 years; OS = 77 days; status (0=alive/1=dead): 1


title: Mouse MF1-044


title: CN_AML Patient 81 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =46 years; OS = 17 days; status (0=alive/1=dead): 1


title: Mouse MF1-040


title: Mouse MF1-042


title: Mouse MF1-039


title: CN_AML Patient 80 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =75 years; OS = 50 days; status (0=alive/1=dead): 1


title: Mouse MF1-041


title: CN_AML Patient 79 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =67 years; OS = 39 days; status (0=alive/1=dead): 1


title: Mouse MF1-038


title: Mouse MF1-037


title: CN_AML Patient 78 (U133B)

description: AML, normal karyotype (training set) FAB M6; age =71 years; OS = 41 days; status (0=alive/1=dead): 1


title: CN_AML Patient 86 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =72 years; OS = 1176 days; status (0=alive/1=dead)


title: Mouse MF1-035


title: Mouse MF1-033


title: CN_AML Patient 76 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =60 years; OS = 256 days; status (0=alive/1=dead): 1


title: Mouse MF1-031

description: Whole genome association analysis of gene expression traits in an outbred mouse population, the MF1 stock.


title: CN_AML Patient 74 (U133B)

description: AML, normal karyotype (training set) FAB M0; age =52 years; OS = 56 days; status (0=alive/1=dead): 1


title: Mouse MF1-028


title: Mouse MF1-025


title: CN_AML Patient 83 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =67 years; OS = 157 days; status (0=alive/1=dead)


title: Mouse MF1-036


title: Mouse MF1-024


title: CN_AML Patient 73 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =27 years; OS = 321 days; status (0=alive/1=dead): 1


title: CN_AML Patient 75 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =69 years; OS = 124 days; status (0=alive/1=dead): 1


title: CN_AML Patient 85 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =60 years; OS = 599 days; status (0=alive/1=dead)


title: Mouse MF1-029


title: CN_AML Patient 80 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =75 years; OS = 50 days; status (0=alive/1=dead)


title: CN_AML Patient 71 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =80 years; OS = 27 days; status (0=alive/1=dead): 1


title: CN_AML Patient 77 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =54 years; OS = 442 days; status (0=alive/1=dead): 1


title: Mouse MF1-017


title: Mouse MF1-030


title: Mouse MF1-022


title: Mouse MF1-020


title: Mouse MF1-018


title: Mouse MF1-027


title: Mouse MF1-019


title: CN_AML Patient 72 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =62 years; OS = 123 days; status (0=alive/1=dead): 1


title: Mouse MF1-016


title: CN_AML Patient 70 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =49 years; OS = 280 days; status (0=alive/1=dead): 1


title: CN_AML Patient 78 (U133A)

tag: AML, normal karyotype (training set) FAB M6; age =71 years; OS = 41 days; status (0=alive/1=dead)


title: CN_AML Patient 79 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =67 years; OS = 39 days; status (0=alive/1=dead)


title: Mouse MF1-015

tag: Strain


title: CN_AML Patient 77 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =54 years; OS = 442 days; status (0=alive/1=dead)


title: CN_AML Patient 69 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =71 years; OS = 236 days; status (0=alive/1=dead): 1


title: CN_AML Patient 76 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =60 years; OS = 256 days; status (0=alive/1=dead)


title: Mouse MF1-014


title: Mouse MF1-008


title: Mouse MF1-011


title: CN_AML Patient 68 (U133B)

description: AML, normal karyotype (training set) FAB M6; age =47 years; OS = 749 days; status (0=alive/1=dead): 1


title: Mouse MF1-009


title: CN_AML Patient 66 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =47 years; OS = 285 days; status (0=alive/1=dead): 0


title: CN_AML Patient 67 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =76 years; OS = 1102 days; status (0=alive/1=dead): 1


title: CN_AML Patient 73 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =27 years; OS = 321 days; status (0=alive/1=dead)


title: Mouse MF1-005


title: Mouse MF1-012


title: CN_AML Patient 75 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =69 years; OS = 124 days; status (0=alive/1=dead)


title: Mouse MF1-006


title: CN_AML Patient 65 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =81 years; OS = 41 days; status (0=alive/1=dead): 1


title: CN_AML Patient 74 (U133A)

tag: AML, normal karyotype (training set) FAB M0; age =52 years; OS = 56 days; status (0=alive/1=dead)


title: CN_AML Patient 71 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =80 years; OS = 27 days; status (0=alive/1=dead)


title: CN_AML Patient 63 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =69 years; OS = 86 days; status (0=alive/1=dead): 1


title: CN_AML Patient 70 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =49 years; OS = 280 days; status (0=alive/1=dead)


title: Mouse MF1-001


title: CN_AML Patient 64 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =46 years; OS = 1176 days; status (0=alive/1=dead): 0


title: Mouse MF1-004


title: CN_AML Patient 72 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =62 years; OS = 123 days; status (0=alive/1=dead)


title: retina-control-rep3

city: Tuebingen

first: Marita

middle: Pauline

last: Feldkaemper

address: Calwerstrasse 7/1

department: Section of Neurobiology of the Eye

institute: University Eye Hospital Tuebingen, Institute for Ophthalmic Research

description: Four samples each: Retina of both eyes of +6.9 diopter lens-treated chicks (plus_lens), Retina of both eyes of untreated control chicks (control)

hyb_protocol: see manufacturer's website

scan_protocol: see manufacturer's website

data_processing: transformation algorithm: GC-RMA

label: Biotin

organism: Gallus gallus

source_name: retina, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (see manufacturer´s website: Expression Analysis Technical Manual, One-Cycle Target Labeling Assay, Affymetrix).

growth_protocol: chicks were raised in groups under a 12-hr light/12-hr dark cycle with free access to food and water. Illumination was provided by light bulbs that produced an ambient illuminance of about 1000 lux on the cage floor.

extract_protocol: The retinae of both eyes were pooled and RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instruction. RNA was quantified and checked for quality with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). The RNA integrity numbers (RIN) ranged from 9.2 to 9.5 (with 1 being the most degraded profile and 10 being the most intact).

treatment_protocol: One day prior to the experiment (age: 8 days), velcro rings were glued to the feathers around the eye under diethylether anaesthesia. At the age of 9 days, after 4-6 hours of light-onset, plus 6.9 diopter lenses were fitted to both eyes of the plus_lens treated group, control chicks received no lenses. 24 hours later, Chicks were killed by an overdose of diethylether, decapitated and the eyes were enucleated. Retinal samples were snap-frozen in liquid nitrogen and stored at -80°C.

value: White Leghorn

tag: Gender

tag: Age

value: 9 days


title: retina-control-rep4


title: Mouse MF1-007


title: CN_AML Patient 62 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =48 years; OS = 31 days; status (0=alive/1=dead): 1


title: CN_AML Patient 60 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =70 years; OS = 252 days; status (0=alive/1=dead): 1


title: CN_AML Patient 57 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =62 years; OS = 30 days; status (0=alive/1=dead): 1


title: retina-plus_lens-rep2

source_name: retina, 24 hours plus 6.9D lens-treated


title: retina-plus_lens-rep1


title: CN_AML Patient 54 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =72 years; OS = 289 days; status (0=alive/1=dead): 1


title: CN_AML Patient 61 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =26 years; OS = 44 days; status (0=alive/1=dead): 1


title: retina-plus_lens-rep4


title: CN_AML Patient 69 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =71 years; OS = 236 days; status (0=alive/1=dead)


title: retina-plus_lens-rep3


title: CN_AML Patient 55 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =66 years; OS = 113 days; status (0=alive/1=dead): 1


title: CN_AML Patient 59 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =40 years; OS = 205 days; status (0=alive/1=dead): 1


title: retina-control-rep1


title: CN_AML Patient 52 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =59 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 51 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =52 years; OS = 283 days; status (0=alive/1=dead): 1


title: CN_AML Patient 68 (U133A)

tag: AML, normal karyotype (training set) FAB M6; age =47 years; OS = 749 days; status (0=alive/1=dead)


title: CN_AML Patient 58 (U133A)

description: AML, normal karyotype (training set) FAB M4; age =43 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 64 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =46 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 49 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =19 years; OS = 826 days; status (0=alive/1=dead): 0


title: CN_AML Patient 53 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =49 years; OS = 61 days; status (0=alive/1=dead): 1


title: CN_AML Patient 61 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =26 years; OS = 44 days; status (0=alive/1=dead)


title: CN_AML Patient 62 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =48 years; OS = 31 days; status (0=alive/1=dead)


title: retina-control-rep2


title: CN_AML Patient 60 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =70 years; OS = 252 days; status (0=alive/1=dead)


title: CN_AML Patient 56 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =54 years; OS = 109 days; status (0=alive/1=dead): 1


title: CN_AML Patient 57 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =62 years; OS = 30 days; status (0=alive/1=dead)


title: CN_AML Patient 58 (U133B)

tag: AML, normal karyotype (training set) FAB M4; age =43 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 59 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =40 years; OS = 205 days; status (0=alive/1=dead)


title: CN_AML Patient 50 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =63 years; OS = 461 days; status (0=alive/1=dead): 1


title: CN_AML Patient 55 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =66 years; OS = 113 days; status (0=alive/1=dead)


title: CN_AML Patient 48 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =73 years; OS = 260 days; status (0=alive/1=dead): 1


title: CN_AML Patient 56 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =54 years; OS = 109 days; status (0=alive/1=dead)


title: CN_AML Patient 47 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =65 years; OS = 47 days; status (0=alive/1=dead): 1


title: CN_AML Patient 54 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =72 years; OS = 289 days; status (0=alive/1=dead)


title: CN_AML Patient 45 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =46 years; OS = 105 days; status (0=alive/1=dead): 1


title: CN_AML Patient 46 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =43 years; OS = 119 days; status (0=alive/1=dead): 1


title: CN_AML Patient 51 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =52 years; OS = 283 days; status (0=alive/1=dead)


title: CN_AML Patient 41 (U133B)

description: AML, normal karyotype (training set) FAB M6; age =34 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 52 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =59 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 42 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =50 years; OS = 247 days; status (0=alive/1=dead): 1


title: CN_AML Patient 49 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =19 years; OS = 826 days; status (0=alive/1=dead)


title: CN_AML Patient 38 (U133B)

description: AML, normal karyotype (training set) FAB M0; age =62 years; OS = 257 days; status (0=alive/1=dead): 1


title: CN_AML Patient 43 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =33 years; OS = 293 days; status (0=alive/1=dead): 1


title: CN_AML Patient 46 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =43 years; OS = 119 days; status (0=alive/1=dead)


title: CN_AML Patient 40 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =47 years; OS = 366 days; status (0=alive/1=dead): 0


title: CN_AML Patient 44 (U133A)

description: AML, normal karyotype (training set) FAB M0; age =34 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 39 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =73 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 53 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =49 years; OS = 61 days; status (0=alive/1=dead)


title: CN_AML Patient 36 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =62 years; OS = 842 days; status (0=alive/1=dead): 0


title: CN_AML Patient 47 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =65 years; OS = 47 days; status (0=alive/1=dead)


title: CN_AML Patient 44 (U133B)

tag: AML, normal karyotype (training set) FAB M0; age =34 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 50 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =63 years; OS = 461 days; status (0=alive/1=dead)


title: CN_AML Patient 45 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =46 years; OS = 105 days; status (0=alive/1=dead)


title: CN_AML Patient 35 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =45 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 37 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =28 years; OS = 425 days; status (0=alive/1=dead): 0


title: CN_AML Patient 34 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =41 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 48 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =73 years; OS = 260 days; status (0=alive/1=dead)


title: CN_AML Patient 42 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =50 years; OS = 247 days; status (0=alive/1=dead)


title: CN_AML Patient 40 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =47 years; OS = 366 days; status (0=alive/1=dead)


title: CN_AML Patient 41 (U133A)

tag: AML, normal karyotype (training set) FAB M6; age =34 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 33 (U133B)

description: AML, normal karyotype (training set) FAB M6; age =55 years; OS = 1103 days; status (0=alive/1=dead): 0


title: CN_AML Patient 31 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =78 years; OS = 4 days; status (0=alive/1=dead): 1


title: CN_AML Patient 32 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =63 years; OS = 18 days; status (0=alive/1=dead): 1


title: CN_AML Patient 37 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =28 years; OS = 425 days; status (0=alive/1=dead)


title: CN_AML Patient 39 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =73 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 36 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =62 years; OS = 842 days; status (0=alive/1=dead)


title: CN_AML Patient 29 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =74 years; OS = 240 days; status (0=alive/1=dead): 1


title: CN_AML Patient 23 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =64 years; OS = 223 days; status (0=alive/1=dead): 1


title: CN_AML Patient 38 (U133A)

tag: AML, normal karyotype (training set) FAB M0; age =62 years; OS = 257 days; status (0=alive/1=dead)


title: CN_AML Patient 35 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =45 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 27 (U133B)

description: AML, normal karyotype (training set) FAB M6; age =76 years; OS = 924 days; status (0=alive/1=dead): 0


title: CN_AML Patient 21 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =66 years; OS = 72 days; status (0=alive/1=dead): 0


title: CN_AML Patient 30 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =54 years; OS = 75 days; status (0=alive/1=dead): 1


title: CN_AML Patient 32 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =63 years; OS = 18 days; status (0=alive/1=dead)


title: CN_AML Patient 24 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =62 years; OS = 214 days; status (0=alive/1=dead): 1


title: CN_AML Patient 25 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =61 years; OS = 33 days; status (0=alive/1=dead): 1


title: CN_AML Patient 33 (U133A)

tag: AML, normal karyotype (training set) FAB M6; age =55 years; OS = 1103 days; status (0=alive/1=dead)


title: CN_AML Patient 26 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =72 years; OS = 3 days; status (0=alive/1=dead): 1


title: CN_AML Patient 27 (U133A)

tag: AML, normal karyotype (training set) FAB M6; age =76 years; OS = 924 days; status (0=alive/1=dead)


title: CN_AML Patient 20 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =66 years; OS = 8 days; status (0=alive/1=dead): 1


title: CN_AML Patient 29 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =74 years; OS = 240 days; status (0=alive/1=dead)


title: CN_AML Patient 28 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =76 years; OS = 1176 days; status (0=alive/1=dead): 0


title: CN_AML Patient 22 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =61 years; OS = 860 days; status (0=alive/1=dead): 0


title: CN_AML Patient 19 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =25 years; OS = 190 days; status (0=alive/1=dead): 1


title: CN_AML Patient 26 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =72 years; OS = 3 days; status (0=alive/1=dead)


title: CN_AML Patient 17 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =48 years; OS = 190 days; status (0=alive/1=dead): 1


title: CN_AML Patient 18 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =26 years; OS = 317 days; status (0=alive/1=dead): 0


title: CN_AML Patient 16 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =49 years; OS = 209 days; status (0=alive/1=dead): 0


title: CN_AML Patient 28 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =76 years; OS = 1176 days; status (0=alive/1=dead)


title: CN_AML Patient 11 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =55 years; OS = 51 days; status (0=alive/1=dead): 1


title: CN_AML Patient 15 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =48 years; OS = 719 days; status (0=alive/1=dead): 0


title: CN_AML Patient 24 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =62 years; OS = 214 days; status (0=alive/1=dead)


title: CN_AML Patient 10 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =56 years; OS = 1 days; status (0=alive/1=dead): 1


title: CN_AML Patient 9 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =48 years; OS = 41 days; status (0=alive/1=dead): 1


title: CN_AML Patient 18 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =26 years; OS = 317 days; status (0=alive/1=dead)


title: CN_AML Patient 16 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =49 years; OS = 209 days; status (0=alive/1=dead)


title: CN_AML Patient 13 (U133B)

description: AML, normal karyotype (training set) FAB M0; age =64 years; OS = 761 days; status (0=alive/1=dead): 1


title: CN_AML Patient 21 (U133A)

description: AML, normal karyotype (training set) FAB M4; age =66 years; OS = 72 days; status (0=alive/1=dead): 0


title: CN_AML Patient 14 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =54 years; OS = 294 days; status (0=alive/1=dead): 1


title: CN_AML Patient 12 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =52 years; OS = 253 days; status (0=alive/1=dead): 1


title: CN_AML Patient 17 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =48 years; OS = 190 days; status (0=alive/1=dead)


title: CN_AML Patient 8 (U133B)

description: AML, normal karyotype (training set) FAB M5; age =34 years; OS = 421 days; status (0=alive/1=dead): 1


title: CN_AML Patient 23 (U133A)

description: AML, normal karyotype (training set) FAB M1; age =64 years; OS = 223 days; status (0=alive/1=dead): 1


title: CN_AML Patient 7 (U133B)

description: AML, normal karyotype (training set) FAB M1; age =66 years; OS = 427 days; status (0=alive/1=dead): 1


title: CN_AML Patient 6 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =52 years; OS = 657 days; status (0=alive/1=dead): 1


title: CN_AML Patient 4 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =66 years; OS = 280 days; status (0=alive/1=dead): 0


title: CN_AML Patient 5 (U133B)

description: MDS RAEB, normal karyotype (training set) MDS RAEB; age =61 years; OS = 275 days; status (0=alive/1=dead): 0


title: CN_AML Patient 15 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =48 years; OS = 719 days; status (0=alive/1=dead)


title: CN_AML Patient 11 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =55 years; OS = 51 days; status (0=alive/1=dead)


title: CN_AML Patient 3 (U133B)

description: AML, normal karyotype (training set) FAB M2; age =66 years; OS = 432 days; status (0=alive/1=dead): 1


title: CN_AML Patient 10 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =56 years; OS = 1 days; status (0=alive/1=dead)


title: CN_AML Patient 14 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =54 years; OS = 294 days; status (0=alive/1=dead)


title: CN_AML Patient 2 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =59 years; OS = 104 days; status (0=alive/1=dead): 0


title: CN_AML Patient 12 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =52 years; OS = 253 days; status (0=alive/1=dead)


title: CN_AML Patient 8 (U133A)

tag: AML, normal karyotype (training set) FAB M5; age =34 years; OS = 421 days; status (0=alive/1=dead)


title: CN_AML Patient 9 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =48 years; OS = 41 days; status (0=alive/1=dead)


title: CN_AML Patient 6 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =52 years; OS = 657 days; status (0=alive/1=dead)


title: CN_AML Patient 7 (U133A)

tag: AML, normal karyotype (training set) FAB M1; age =66 years; OS = 427 days; status (0=alive/1=dead)


title: CN_AML Patient 4 (U133A)

tag: AML, normal karyotype (training set) FAB M4; age =66 years; OS = 280 days; status (0=alive/1=dead)


title: CN_AML Patient 1 (U133B)

description: AML, normal karyotype (training set) FAB M4; age =62 years; OS = 4 days; status (0=alive/1=dead): 1


title: CN_AML Patient 3 (U133A)

tag: AML, normal karyotype (training set) FAB M2; age =66 years; OS = 432 days; status (0=alive/1=dead)


status: Public on Aug 21 2008

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

description:
Fadrozole 7 d brain pooled sample number BF2
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

hyb_protocol: The microarrays were hybridized in Agilent hybridization chambers and incubated overnight (17 h) in a hybridization oven (Model G2545A, Agilent) at 60°C. The following day, slides were washed for 1 min in 6X SSPE, 0.005% N-laurosylsarcosine; 1 min in 0.06X SSPE, 0.005% N-laurosylsarcosine; and then dried by dipping in a stabilization and drying solution for 30 s

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and raw images processed using Agilent’s Feature Extraction Software, Version 8.1.

data_processing: Data were first filtered to remove flagged features (e.g., saturated, nonuniform spots).  Following filtering, data from each spot was local background subtracted, Lowess normalized, and log transformed (base 10).

organism: Pimephales promelas

source_name: female brain, exposed to 60 ug/L fadrozole for 7 day

label_protocol: cRNA was labeled with Cyanine 5 (experimental samples) using Agilent's low-input fluorescent linear amplification kit (for additional details see Larkin et al.  2007).  Amplification yields and dye incorporation were quantified using a Nanodrop spectrophotometer

growth_protocol: 25°C, 16:8 light:dark photoperiod, fed adult brine shrimp twice daily

extract_protocol: Total RNA was isolated from tissue samples using TRI Reagent lysis solution (Molecular Research Center, Cincinnati, OH, USA) following the manufacturer's protocol.  Samples were DNAse treated and quality of the total RNA was evaluated by denaturing-agarose gel eletrophoresis and optical density (260/280 ratio 1.8-2.0).  Aliquots of total RNA extracted from the liver or brain of two females from the same replicate tank were pooled and poly-A RNA was reverse transcribed from 500 ng of pooled total RNA using a poly dT-T7 primer

treatment_protocol: fish were humanely euthanized in buffered tricaine methanesulfonate (Finquel; Argent, Redmond, WA, USA).  Liver samples were then collected and transferred directly to pre-weighed vials containing RNAlater® (Sigma, St. Louis, MO).

tag: Gender

value: Female

tag: Age

value: 6 months

tag: Strain

value: wild-type

tag: Tissue

value: Brain

tag: Sample

value: Total RNA pooled from n=2 fish

tag: Expt id of fish pooled

tag: Fish Mass

source_name: pooled liver, brain, and gonad samples from adult male and female fathead minnows

label_protocol: cRNA was labeled with Cyanine 3 (reference samples) using Agilent's low-input fluorescent linear amplification kit.  Amplification yields and dye incorporation were quantified using a Nanodrop spectrophotometer


title: Fadrozole 7 d brain pooled sample number BF3

description:
Fadrozole 7 d brain pooled sample number 7BH3
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

extract_protocol: Total RNA was isolated from tissue samples using TRI Reagent lysis solution (Molecular Research Center, Cincinnati, OH, USA) following the manufacturer's protocol.  Samples were DNAse treated and quality of the total RNA was evaluated by denaturing-agarose gel eletrophoresis and optical density (260/280 ratio 1.8-2.0).

tag: pooled liver, brain, and gonad samples from adult male and female fathead minnows


description:
Control 7 d liver pooled sample number LC1
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

source_name: female liver, exposed to control water for 7 day

value: Liver


description:
Control 7 d brain pooled sample number BC1
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

source_name: female brain, exposed to control water for 7 day


title: Cancer tissue for ID_113

type: genomic

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

country: Japan

institute: Jichi Medical University

description: no additional information

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner 3000, GCOS 1.2

data_processing: DAT and CEL files were processed by Affymetrix GCOS 1.2 with default analysis settings. Calls generated by GDAS 3.0 with confidence threshold 0.05.

source_name: Colorectal tissue

label_protocol: Standard Affymetrix procedures

extract_protocol: Extraction of genomic DNA with high molecular weight was performed using QIamp micro DNA extraction kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: disease_state = Carcinoma

tag: Patient_ID = ID_113

tag: Sex = F

tag: Position = Left

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1278

tag: Censor = Yes


title: Normal tissue for ID_110

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_110

tag: Age = 76

tag: Sex = M

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1288


title: Normal tissue for ID_112

description: no additional information

tag: Patient_ID = ID_112

tag: Position = Rectum

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1280


description:
Fadrozole 7 d brain pooled sample number BF1
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

tag: Gender

tag: Age

tag: Strain

tag: Tissue

tag: Sample

tag: Expt id of fish pooled

tag: Fish Mass

tag: pooled liver, brain, and gonad samples from adult male and female fathead minnows


title: Cancer tissue for ID_115

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_115

tag: Sex = F

tag: Position = Right

tag: MSI = No

tag: Observation_(days) = 435

tag: Censor = No


description:
Control 7 d liver pooled sample number LC2
mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Normal tissue for ID_115

description: no additional information

tag: disease_state = Normal

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes


description:
Control 7 d liver pooled sample number LC3
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

tag: Gender

tag: Age

tag: Strain


title: Cancer tissue for ID_112

description: no additional information

tag: Patient_ID = ID_112

tag: Sex = M

tag: Position = Rectum

tag: Observation_(days) = 1280

tag: Censor = Yes


description:
Fadrozole 7 d liver pooled sample number LF3
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

source_name: female liver, exposed to 60 ug/L fadrozole for 7 day

tag: Tissue

tag: Sample

tag: Expt id of fish pooled

tag: Fish Mass

tag: pooled liver, brain, and gonad samples from adult male and female fathead minnows


description:
Control 7 d brain pooled sample number BC3
mention of trade names or commercial products does not constitute endorsement or recommendation for use.


title: Normal tissue for ID_113

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_113

tag: Sex = F

tag: Position = Left

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1278


description:
Fadrozole 7 d liver pooled sample number LF2
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

tag: Gender

tag: Age

tag: Strain


title: Control 7 d brain pooled sample number BC2

description:
Control 7 d brain pooled sample number 7BC2
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

tag: Tissue


title: Normal tissue for ID_109

description: no additional information

tag: Patient_ID = ID_109

tag: Age = 74

tag: Position = Rectum

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1301

tag: Censor = Yes


title: Cancer tissue for ID_109

description: no additional information

tag: disease_state = Carcinoma

tag: Sex = F


title: Cancer tissue for ID_108

description: no additional information

tag: Patient_ID = ID_108

tag: Sex = M

tag: Position = Left

tag: Pathology = moderately differentiated adenocarcinoma


title: Smad5MOB

city: Bronx

first: Lisa

middle: J.

last: McReynolds

state: NY

address: 1300 Morris Park Ave. Chanin 501

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

description: set B

hyb_protocol: Nimblegen

scan_protocol: Nimblegen

data_processing: Data normalized using NimbleScan. Log2 ratios (experimental/wildtype) determined using R analysis software.

source_name: Smad5 morphant

label_protocol: Nimblegen

extract_protocol: Qiagen RNeasy Mini Kit

tag: Smad5 morphant, 1-somite embryo

source_name: Wildtype

tag: Wildtype, 1-somite embryo


title: Cancer tissue for ID_110

description: no additional information

tag: Patient_ID = ID_110

tag: Age = 76

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1288


title: Normal tissue for ID_108

description: no additional information

tag: disease_state = Normal

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1301


title: Normal tissue for ID_103

description: no additional information

tag: Patient_ID = ID_103

tag: Position = Rectum

tag: Observation_(days) = 1343

tag: Censor = Yes


description:
Fadrozole 7 d liver pooled sample number LF1
mention of trade names or commercial products does not constitute endorsement or recommendation for use.

tag: Gender

tag: Age

tag: Strain

tag: Tissue

tag: Sample

tag: Expt id of fish pooled

tag: Fish Mass

tag: pooled liver, brain, and gonad samples from adult male and female fathead minnows


title: Cancer tissue for ID_102

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_102

tag: Sex = M

tag: Pathology = moderately differentiated adenocarcinoma

tag: MSI = No

tag: Observation_(days) = 76


title: Cancer tissue for ID_105

description: no additional information

tag: Patient_ID = ID_105

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1341


title: Cancer tissue for ID_107

description: no additional information

tag: Patient_ID = ID_107

tag: Age = 73

tag: Observation_(days) = 1327

tag: Censor = Yes


title: Normal tissue for ID_106

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_106

tag: Sex = F

tag: Position = Rectum

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1330


title: Cancer tissue for ID_099

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_099

tag: Position = Right

tag: Pathology = moderately differentiated adenocarcinoma

tag: MSI = No

tag: Observation_(days) = 1349


title: Normal tissue for ID_102

description: no additional information

tag: Patient_ID = ID_102

tag: Sex = M

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 76


title: Normal tissue for ID_099

description: no additional information

tag: disease_state = Normal

tag: Censor = Yes


title: Cancer tissue for ID_103

description: no additional information

tag: Patient_ID = ID_103

tag: Position = Rectum

tag: Observation_(days) = 1343


title: Normal tissue for ID_105

description: no additional information

tag: Patient_ID = ID_105

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1341


title: Smad1MOE

description: set E

source_name: Smad1 morphant

tag: Smad1 morphant, 1-somite embryo

tag: Wildtype, 1-somite embryo


title: Cancer tissue for ID_098

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_098

tag: Sex = F

tag: Duke's_grade = D

tag: MSI = No

tag: Observation_(days) = 902

tag: Censor = No


title: Normal tissue for ID_107

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_107

tag: Age = 73

tag: Sex = M

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1327

tag: Censor = Yes


title: Cancer tissue for ID_097

description: no additional information

tag: Patient_ID = ID_097

tag: Position = Left

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1351


title: Normal tissue for ID_096

description: no additional information

tag: Patient_ID = ID_096

tag: Sex = F

tag: Duke's_grade = D

tag: MSI = No


title: Smad1MOA

description: set A

tag: Smad1 morphant, 1-somite embryo

tag: Wildtype, 1-somite embryo


title: SmadDKD15H

description: set H

source_name: Smad 1+5 double morphant

tag: Smad 1+5 double morphant, 1-somite embryo


title: SmadDKD15I

description: set I


title: Cancer tissue for ID_096

description: no additional information

tag: disease_state = Carcinoma


title: Normal tissue for ID_097

description: no additional information

tag: disease_state = Normal

tag: Sex = M


title: SmadDKD15G

description: set G


title: Smad5MOF

description: set F

tag: Smad5 morphant, 1-somite embryo


title: Smad1MOD

description: set D


title: Cancer tissue for ID_094

description: no additional information

tag: Patient_ID = ID_094

tag: Position = Rectum

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1354

tag: Censor = Yes


title: Normal tissue for ID_095

description: no additional information

tag: Patient_ID = ID_095

tag: Position = Left

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 583

tag: Censor = No


title: Normal tissue for ID_094

description: no additional information

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No


title: Cancer tissue for ID_091

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_091

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = D

tag: Observation_(days) = 1331


title: Smad5MOC

description: set C

tag: Smad5 morphant, 1-somite embryo

tag: Wildtype, 1-somite embryo


title: Cancer tissue for ID_090

description: no additional information

tag: Patient_ID = ID_090

tag: Sex = M

tag: Position = Rectum

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1365


title: Cancer tissue for ID_095

description: no additional information

tag: Patient_ID = ID_095

tag: Sex = F

tag: Position = Left

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 583


title: Cancer tissue for ID_092

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_092

tag: Duke's_grade = C

tag: MSI = No

tag: Observation_(days) = 1358

tag: Censor = Yes


title: Normal tissue for ID_093

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_093

tag: Position = Right

tag: Observation_(days) = 1355


title: Normal tissue for ID_091

description: no additional information

tag: Patient_ID = ID_091

tag: Sex = M

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = D

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1331

tag: Censor = No


title: Cancer tissue for ID_088

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_088

tag: Position = Rectum

tag: Pathology = well differentiated adenocarcinoma

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1376


title: Normal tissue for ID_090

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_090

tag: Duke's_grade = B

tag: MSI = No

tag: Observation_(days) = 1365

tag: Censor = Yes


title: Normal tissue for ID_088

description: no additional information

tag: Sex = M

tag: Duke's_grade = C


title: Cancer tissue for ID_089

description: no additional information

tag: Patient_ID = ID_089

tag: Sex = F

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 1371


title: Normal tissue for ID_086

description: no additional information

tag: Patient_ID = ID_086

tag: Position = Right

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1383


title: Normal tissue for ID_085

description: no additional information

tag: Patient_ID = ID_085

tag: Position = Rectum

tag: Pathology = well differentiated adenocarcinoma

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 261


title: Normal tissue for ID_087

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_087

tag: Duke's_grade = B

tag: MSI = No

tag: Observation_(days) = 1378


title: Cancer tissue for ID_085

description: no additional information

tag: disease_state = Carcinoma

tag: Sex = M

tag: Duke's_grade = C

tag: Censor = Yes


title: Normal tissue for ID_089

description: no additional information

tag: Patient_ID = ID_089

tag: Sex = F

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 1371


title: Cancer tissue for ID_086

description: no additional information

tag: Patient_ID = ID_086

tag: Position = Right

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1383


title: Normal tissue for ID_084

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_084

tag: Position = Rectum

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1386


title: Cancer tissue for ID_083

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_083

tag: Lymph_node_metastasis = Yes

tag: MSI = No

tag: Observation_(days) = 1392


title: Cancer tissue for ID_081

description: no additional information

tag: Patient_ID = ID_081

tag: Age = 51

tag: Sex = M

tag: Position = Left

tag: Duke's_grade = C

tag: Observation_(days) = 1404

tag: Censor = Yes


title: Cancer tissue for ID_084

description: no additional information

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No


title: Normal tissue for ID_081

description: no additional information

tag: disease_state = Normal

tag: Pathology = moderately differentiated adenocarcinoma


title: Cancer tissue for ID_093

description: no additional information

tag: Patient_ID = ID_093

tag: Sex = F

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1355


title: Cancer tissue for ID_106

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_106

tag: Position = Rectum

tag: MSI = No

tag: Observation_(days) = 1330


title: Cancer tissue for ID_087

description: no additional information

tag: Patient_ID = ID_087

tag: Sex = M

tag: Observation_(days) = 1378


title: Normal tissue for ID_083

description: no additional information

tag: Patient_ID = ID_083

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1392

tag: Censor = Yes


title: Normal tissue for ID_098

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_098

tag: Sex = F

tag: Duke's_grade = D

tag: Observation_(days) = 902

tag: Censor = No


title: Normal tissue for ID_078

description: no additional information

tag: Patient_ID = ID_078

tag: Position = Rectum

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1407


title: Cancer tissue for ID_080

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_080

tag: MSI = No

tag: Observation_(days) = 1406


title: Cancer tissue for ID_079

description: no additional information

tag: Patient_ID = ID_079

tag: Sex = M

tag: Position = Right

tag: Pathology = poorly differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 59


title: Cancer tissue for ID_077

description: no additional information

tag: Patient_ID = ID_077

tag: Sex = F

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 783

tag: Censor = Yes


title: Normal tissue for ID_075

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_075

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1421


title: Normal tissue for ID_079

description: no additional information

tag: Patient_ID = ID_079

tag: MSI = No

tag: Censor = No


title: Normal tissue for ID_077

description: no additional information

tag: Position = Right


title: Cancer tissue for ID_076

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_076

tag: Sex = M

tag: Position = Rectum

tag: Duke's_grade = A

tag: Observation_(days) = 1420


title: Normal tissue for ID_071

description: no additional information

tag: Patient_ID = ID_071

tag: Sex = F

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 521


title: Cancer tissue for ID_078

description: no additional information

tag: Patient_ID = ID_078

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1407

tag: Censor = Yes


title: Normal tissue for ID_074

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_074

tag: Sex = M

tag: MSI = No

tag: Observation_(days) = 1425


title: Normal tissue for ID_080

description: no additional information

tag: Patient_ID = ID_080

tag: Sex = F

tag: Position = Rectum

tag: Observation_(days) = 1406


title: Cancer tissue for ID_074

description: no additional information

tag: disease_state = Carcinoma

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes


title: Normal tissue for ID_076

description: no additional information

tag: Patient_ID = ID_076

tag: Duke's_grade = A

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1420


title: Cancer tissue for ID_075

description: no additional information

tag: Patient_ID = ID_075

tag: Position = Right

tag: Duke's_grade = B

tag: Observation_(days) = 1421

tag: Censor = Yes


title: Cancer tissue for ID_070

description: no additional information

tag: Patient_ID = ID_070

tag: Age = 70

tag: Sex = M

tag: MSI = No

tag: Observation_(days) = 1439


title: Cancer tissue for ID_073

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_073

tag: Position = Left

tag: Pathology = mucinous adenocarcinoma

tag: Observation_(days) = 1428


title: Normal tissue for ID_067

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_067

tag: Sex = F

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1455


title: Cancer tissue for ID_066

description: no additional information

tag: Patient_ID = ID_066

tag: Position = Rectum

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 1456

tag: Censor = Yes


title: Normal tissue for ID_073

description: no additional information

tag: Sex = M

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No


title: Cancer tissue for ID_071

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_071

tag: Position = Left

tag: Observation_(days) = 521

tag: Censor = No


title: Normal tissue for ID_069

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_069

tag: Position = Right

tag: Observation_(days) = 1453


title: Cancer tissue for ID_067

description: no additional information

tag: Patient_ID = ID_067

tag: Sex = F

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1455


title: Normal tissue for ID_092

description: no additional information

tag: Patient_ID = ID_092

tag: Position = Rectum

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 1358

tag: Censor = Yes


title: Normal tissue for ID_070

description: no additional information

tag: Patient_ID = ID_070

tag: Age = 70

tag: Sex = M

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1439


title: Cancer tissue for ID_069

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_069

tag: Position = Right

tag: Observation_(days) = 1453


title: Normal tissue for ID_066

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_066

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1456


title: Normal tissue for ID_065

description: no additional information

tag: Patient_ID = ID_065

tag: Position = Rectum

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 1459

tag: Censor = Yes


title: Normal tissue for ID_064

description: no additional information

tag: Patient_ID = ID_064

tag: Sex = F

tag: Pathology = mucinous adenocarcinoma

tag: Observation_(days) = 1056

tag: Censor = No


title: Cancer tissue for ID_064

description: no additional information

tag: disease_state = Carcinoma

tag: Position = Right

tag: MSI = No


title: Normal tissue for ID_063

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_063

tag: Sex = M

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1460


title: Normal tissue for ID_060

description: no additional information

tag: Patient_ID = ID_060

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1463

tag: Censor = Yes


title: Cancer tissue for ID_059

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_059

tag: Observation_(days) = 281

tag: Censor = No


title: Normal tissue for ID_061

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_061

tag: Position = Rectum

tag: Duke's_grade = D

tag: MSI = No

tag: Observation_(days) = 1462


title: Cancer tissue for ID_065

description: no additional information

tag: Patient_ID = ID_065

tag: Sex = M

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1459


title: Normal tissue for ID_057

description: no additional information

tag: Patient_ID = ID_057

tag: Sex = F

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1483


title: Cancer tissue for ID_063

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_063

tag: Position = Left

tag: Observation_(days) = 1460

tag: Censor = Yes


title: Cancer tissue for ID_053

description: no additional information

tag: Patient_ID = ID_053

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: MSI = No

tag: Observation_(days) = 570

tag: Censor = No


title: Cancer tissue for ID_060

description: no additional information

tag: Patient_ID = ID_060

tag: Observation_(days) = 1463


title: Normal tissue for ID_059

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_059

tag: Sex = M

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 281


title: Cancer tissue for ID_061

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_061

tag: Position = Rectum

tag: Duke's_grade = D

tag: Observation_(days) = 1462


title: Cancer tissue for ID_057

description: no additional information

tag: Patient_ID = ID_057

tag: Sex = F

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1483

tag: Censor = Yes


title: Normal tissue for ID_051

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_051

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: MSI = No

tag: Observation_(days) = 1505


title: Cancer tissue for ID_056

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_056

tag: Sex = M

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No


title: Normal tissue for ID_056

description: no additional information

tag: Position = Rectum


title: Normal tissue for ID_050

description: no additional information

tag: Patient_ID = ID_050

tag: Position = Right


title: Cancer tissue for ID_049

description: no additional information

tag: Patient_ID = ID_049

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma


title: Normal tissue for ID_046

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_046

tag: Sex = F

tag: Duke's_grade = D

tag: Observation_(days) = 542

tag: Censor = No


title: Cancer tissue for ID_046

description: no additional information

tag: disease_state = Carcinoma

tag: MSI = No


title: Normal tissue for ID_047

description: no additional information

tag: Patient_ID = ID_047

tag: Sex = M

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1525

tag: Censor = Yes


title: Cancer tissue for ID_051

description: no additional information

tag: Patient_ID = ID_051

tag: Position = Rectum

tag: Observation_(days) = 1505


title: Normal tissue for ID_053

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_053

tag: Position = Left

tag: Observation_(days) = 570


title: Cancer tissue for ID_048

description: no additional information

tag: Patient_ID = ID_048

tag: Sex = F

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1512


title: Normal tissue for ID_049

description: no additional information

tag: Patient_ID = ID_049

tag: Sex = M

tag: MSI = No


title: Cancer tissue for ID_047

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_047

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1525

tag: Censor = Yes


title: Normal tissue for ID_045

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_045

tag: Pathology = mucinous adenocarcinoma

tag: Observation_(days) = 1365

tag: Censor = No